Variant report

Variant	rs4924478
Chromosome Location	chr15:40818499-40818500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40818208..40820225-chr15:40824846..40826770,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPUSD2-2	chr15:40817905-40821053	ucscGeneNc_uc001zqm_2

Extended variants
information (count: 103 )
Associated
traits (count: 32 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1037445	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10400890	0.82[EUR][1000 genomes]
rs10467972	0.80[JPT][hapmap]
rs11070275	1.00[CEU][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070277	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070282	0.81[EUR][1000 genomes]
rs11070285	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs11070286	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs11632061	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11632370	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11638742	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639464	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11852670	0.82[EUR][1000 genomes]
rs11852694	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11852828	0.82[EUR][1000 genomes]
rs11854986	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11855334	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs11855923	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs11856438	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11856802	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs11858113	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs12591207	0.81[EUR][1000 genomes]
rs12594548	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12595610	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905162	0.96[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12912058	0.80[JPT][hapmap]
rs12914743	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs12916042	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12916323	0.80[CEU][hapmap]
rs16970851	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs1806961	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1811513	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1813898	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1869301	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1869302	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1967368	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1993212	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2034651	0.96[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2034652	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2167795	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2278888	0.80[JPT][hapmap]
rs2412531	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412532	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2412541	0.80[JPT][hapmap]
rs2412544	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs2444302	0.96[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2898996	0.81[EUR][1000 genomes]
rs2924386	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2924387	0.85[EUR][1000 genomes]
rs2924388	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2959536	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2959545	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3092978	0.80[JPT][hapmap]
rs3092979	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs35047458	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs3751652	0.81[EUR][1000 genomes]
rs3751653	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs4080706	0.82[EUR][1000 genomes]
rs4923875	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4923876	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924472	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924479	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4924480	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4924481	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924488	0.80[JPT][hapmap]
rs588686	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs590046	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs603623	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs616937	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs618399	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs619711	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs620198	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6492947	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs6492951	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492958	1.00[YRI][hapmap]
rs654317	0.85[EUR][1000 genomes]
rs6582	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71471881	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7167417	0.80[JPT][hapmap]
rs7169621	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7171260	0.80[JPT][hapmap]
rs7177192	0.80[JPT][hapmap]
rs7178756	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7183273	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7494968	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026605	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8028999	0.80[JPT][hapmap]
rs8029384	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034326	0.81[EUR][1000 genomes]
rs8035775	0.80[JPT][hapmap]
rs8036737	0.83[EUR][1000 genomes]
rs8037804	0.80[JPT][hapmap]
rs8038407	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8040502	0.80[JPT][hapmap]
rs8041534	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs8042729	0.84[JPT][hapmap]
rs896795	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs896796	1.00[YRI][hapmap]
rs9652415	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs976401	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:32)

SNP	Gene	Cis/trans	Tissue	Source
rs4924478	C15orf57	cis	Cerebellum	GTEx
rs4924478	C15orf57	cis	Heart Left Ventricle	GTEx
rs4924478	CCDC32	cis	normal skin	skin_eQTL
rs4924478	C15orf57	cis	Artery Tibial	GTEx
rs4924478	C15orf57	cis	lymphoblastoid	seeQTL
rs4924478	DISP2	cis	parietal	SCAN
rs4924478	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs4924478	C15orf57	cis	Nerve Tibial	GTEx
rs4924478	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs4924478	C15orf57	cis	Muscle Skeletal	GTEx
rs4924478	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs4924478	C15orf57	cis	Esophagus Muscularis	GTEx
rs4924478	LPCAT4	cis	parietal	SCAN
rs4924478	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs4924478	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs4924478	PLA2G4E	cis	parietal	SCAN
rs4924478	CCDC32	cis	multi-tissue	Pritchard
rs4924478	C15orf57	cis	parietal	SCAN
rs4924478	C15orf57	cis	Esophagus Mucosa	GTEx
rs4924478	IVD	cis	cerebellum	SCAN
rs4924478	RP11-111A22.1	cis	Artery Tibial	GTEx
rs4924478	C15orf57	cis	Adipose Subcutaneous	GTEx
rs4924478	CCDC32	cis	lesional skin	skin_eQTL
rs4924478	C15orf23	cis	cerebellum	SCAN
rs4924478	C15orf57	cis	Artery Aorta	GTEx
rs4924478	C15orf57	cis	cerebellum	SCAN
rs4924478	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs4924478	ZFYVE19	cis	cerebellum	SCAN
rs4924478	RP11-111A22.1	cis	lung	GTEx
rs4924478	C15orf57	cis	lung	GTEx
rs4924478	ITPKA	cis	parietal	SCAN
rs4924478	ZFYVE19	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40804400-40821000	Weak transcription	Right Atrium	heart
2	chr15:40805200-40828200	Weak transcription	Placenta	Placenta
3	chr15:40805200-40833000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:40812400-40818800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:40812400-40820200	Weak transcription	Fetal Stomach	stomach
6	chr15:40812400-40828600	Weak transcription	Primary T cells from cord blood	blood
7	chr15:40812400-40828600	Weak transcription	Right Ventricle	heart
8	chr15:40812400-40828800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:40812400-40828800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:40812400-40829000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:40812400-40829000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:40812400-40831000	Weak transcription	Thymus	Thymus
13	chr15:40812400-40837800	Weak transcription	Lung	lung
14	chr15:40812600-40826000	Weak transcription	Adipose Nuclei	Adipose
15	chr15:40812600-40826400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr15:40812600-40827000	Weak transcription	Spleen	Spleen
17	chr15:40812600-40831400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:40812600-40840600	Weak transcription	Hela-S3	cervix
19	chr15:40816200-40820600	Weak transcription	Fetal Intestine Small	intestine
20	chr15:40816600-40826200	Weak transcription	GM12878-XiMat	blood
21	chr15:40816800-40835000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr15:40816800-40845600	Weak transcription	Ovary	ovary
23	chr15:40817800-40819600	Enhancers	Pancreas	Pancrea
24	chr15:40817800-40821800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr15:40818200-40819400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr15:40818200-40828000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr15:40818400-40820600	Weak transcription	K562	blood
28	chr15:40818400-40828200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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